Biological Filtration

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Biological filtration.

The next stage after the removal of the solids is the reduction of dissolved waste such as ammonia and nitrite. The biological filter is an area devoted to the support and concentration of bacteria needed to break down the waste.
The waste from the fish is the start of the nitrogen cycle in the pond this is an important biological cycle that nature uses to recycle the waste that the fish produce.

simplified nitrogen cycleThe figure shown is a very simplified one and shows the basic actions in the cycle.
The start is when the fish are fed with food, they covert it in to body mass and use some as energy to live, the waste is excreted in the form of ammonia. The naturally occurring bacteria in the pond, nitrosomonas, break ammonia down to nitrite using oxygen. Once this has been done the next set of bacteria, nirtobacter, get to work converting nitrite to nitrate, this process also requires oxygen.
The final product nitrate is plant food and the pond plants good and bad(algae) need this to grow and will consume as much as they can. The nitrate level will rise as it is unlikely that the plants in the pond will be able to keep up with the nitrate production.

What Bacteria Want.

The bacteria have a few simple requirements , the first being oxygen, this is needed to break down ammonia to nitrite and nitrite to nitrate.The food required is readily supplied by the fish in the form of ammonia.
The important issues that effect biological filters are :

The filter media.

The filter media is the bacteria's home and should offer a large surface area as the more bacteria you can support the more work the filter can achieve. The media needs to be rough so that the bacteria can grow on the surface. It must have a good structure so that water flows evenly through it so that no dead areas can become anaerobic (oxygen deficient).

There are a huge variation of medias on the market today ranging from lava rock to plastic sheeting.
All need to fill the basic needs of a good filter media, they should compile with all of them.

The first media available to pond keepers was gravel and now the choice has become some what difficult, but there is a simple method to choosing the media for you.

A cheap media but shows most of the problems shown above, it compacts down , it is difficult to clean and very heavy.
Aqua rock
This is either crushed lava rock or clinker , the waste out of kilns, and is very difficult to clean and has a poor surface area to volume ratio, and very difficult to clean.
An expanded clay pellet that has a large porous surface area and often floats, can be difficult to clean and clogs easily.
A plastic media created for sewage farms, very good surface area to volume area and relatively inexpensive, used on commercial fish farms. The light weight makes filter construction easy and it is easy to handle. The only down side is that as a loose media it traps dirty and is quite difficult to clean.

Japanese filter mat is a jumble of plastic fibres bonded together. While recommended by fish retailers and koi experts it is a relatively poor media as it has a number of basic problems. It is glued together and the glue eventually fails leading to small plastic fibres floating around the filters and finding their way to the pump which they then clog. It has a random construction and no set surface to volume ratio. The mat is a mix of different plastics and no data is available on the make up of it. The mat needs to be cut up and turned into cartridges as it clogs quickly otherwise.
It is difficult to clean.

Plastic media.
There are a number on the market but many have problems when it comes to the surface, as it is cheaper to produce a media with a smooth surface so most do. This leaves the bacteria with nothing to hang on to, this type of media will take a very long time to a mature. If the water flow is to strong the bacteria will get washed off.

Bio balls.
One of the first effective plastic medias, can only be used in a filter where the first stages remove all the solids as it clogs quite quickly and they are difficult to clean. They offer a very large surface area , but the complex nature of the design is difficult to produce and this is reflected in the very high production cost. Best used in trickle towers.

Bio glass.
A very expensive media as it is a honeycomb of glass, made into small sections in the shape of a doughnut. The surface area is incredibly large ,about 100 times the area per m3 of most other medias . As with most good things it has never proven its self in ponds due to the high particle waste levels in the water , as the surface of the media is so fine it clogs almost on day one and is of little use after a few weeks. It is ideally suited for indoor tanks.

Ready made filters.

The simplest filters consists of a foam prefilter on the front of the pump, these work in small ponds up to 500 litres. They require regular maintenance and if left too long will starve the pump of water and cause the pump to fail. Not really suitable for ponds where lots of fish are housed due to the relatively poor filter capacity and high maintenance.

The next step up in filters consist of a plastic water tank with a spray bar spreading the water across thin sheets of foam of varying grades this collects the particles and any dirt in the water, for the biological action to take place a plastic ring material, which offers a large surface area to a volume ratio, is used for bacteria to live on .

The next stage is a multi-chamber filter. In this type of filter the different filtration stages are split up this allows the use of more media and when cleaning the biological media is left undisturbed.

The filter shown is a simple 3 chamber model that use brushes in the first chamber for settlement and then has two biological chambers for the bacteria, this offers the chance of using two different medias which means that a more diverse habitats for the bacteria to grow in, this will improve the filters efficiency. There is a perforated tray to hold up the media and allow the water to flow underneath to the next chamber. The settlement chamber has a drain to waste for easy maintenance.

The multiple vortex filters are a newer design popular with manufactures as they are cheaper to produce and stronger than ‘box’ shaped filters.

The come in 3, 4 or 5 chamber styles and the media choice is up to you. The vortexes are normally very small and the flow rates recommended are far to quick. To get the best from these it is best to buy larger than suggested by the manufacturers and slow the flow rate down. All chambers have drains making cleaning easy and quick.

They are best used as gravity fed filters other wise the pump breaks up the solids making the collection more difficult.

Fluidised filter beds.
These are biological only and required a good prefilter to stop solids from entering the filter system. They are very effective and very compact for what the capacity they have. They have a set of requirements that must be provided for them to work.
They need a high capacity pump to start and lift the media into suspension.

The flow rate must be constant any large variation will stop the filter from functioning. To much and the media will end up in the pond and to little and the media settles out and will turn anaerobic.

They required well oxygenated water to function as a vast amount of bacteria is held in a very small volume.

The filter must be vertical to work correctly, otherwise the media will settle out on one side creating an anaerobic section.

They must never be used with out a normal biological filter as they are by nature unreliable, and should be considered an additional filter not the main one.

They are effected by chemicals and die quickly if the water flow stops as the media stops moving and sinks to the bottom, compacts down and the bacteria run out of oxygen.

Fludised filters are normally the domain of marine systems and commercial indoor recirculation systems but they are always used as an additional filter because of their difficult nature.

The materials used to build them should be stainless steel or a tough industrial plastic, the nature of the filter with moving sand particles makes them very hard on the filter container and they will soon wear out thin plastic or fibreglass tanks.

Trickle towers.
In the commercial world these are the most popular as they offer the best of all filter methods, again they offer only biological filtration.

As the media is suspended in air, the oxygen content is about 20 times higher than in water so can support 20 times the bacteria of a traditional submerged filter. The action of water falling down the media exposes it the to air helping to remove ammonia which is lost to the atmosphere as a gas and this reduces the work the filter has to do and at the same time reduces nitrate, which in turn reduces algae growth as there is less food for it.

The design is simple and reliable it has few requirements and because of this is easy to set up and run.

The tower can be light weight as it holds no water and only has to hold the filter media up right and contain any water as it falls through the media. It is even possible to use thin plastic sheeting as a tower if the media will self support. This reduces the initial out lay.

The spray bar needs to spread the water evenly over the surface of the media this can be achieved best with a rotating spray bar as it is constantly moving the water across the surface and as it is not a continuous stream it does not wash the bacteria off the media. Other methods such as a spreader plate, which is made up of a tray with holes drilled at set distances all over the base which allows the water to spread over the media.

The filters height needs to be around 1.2m minimum to have any real effect.

The filters efficiency can be improved as the fish increase in size by simply adding an air pump to the filter base so that air is allowed to work its way up the filter and out of the top, this increases the oxygen levels and removes any ammonia that is forced out of the water.

Another easy way to increase the air flow is to add an extractor fan to the tower to pull air through the media.

The two draw backs of trickle towers are height they need to be tall to work and they have to be above the water level of the pond, the second is winter as they pass water through the air they will exchange energy between them , in warm weather they will heat the water, and in cold weather they will cool the water.

If power is lost they can survive undamaged for days with out much loss of efficiency, as the air in the tower is humid and full of oxygen.

Bead Filters.
Bead filters are not a new filter, but have only recently become available to the pond keeper.

A simple principle of using small floating plastic ‘beads’, about 3-4mm in diameter, to act as both a mechanical and biological filter all in one.The design makes them very compact and easy to hide. They are also easy to clean as a simple timer that switches the pump off for 15 minutes a day will start its cleaning cycle. A good prefilter is needed to remove any trace of blanket weed or particles larger than 5mm as these will otherwise clog the inlet strainer, and reduce the through put of water.
The hour glass shape as become the trade mark of the best models as they clean them selves with out the use of any moving parts and have proved to be very reliable.

NOTE: The sludge valve can be replaced with an automatic valve that opens as soon as the pump is switched off this means the filter unit can be left to self clean and restart.

They are slow to start working and seem to suffer if chemicals are added to the pond. Once established the bead filter is good filter. Use units that are larger than recommended as they under perform compared to the manufactures figures.

They are ideal if time is limited and you go away regular as the self cleaning makes maintenance very simple.

Starting the biological filter.
All biological filters take time to processing waste as the bacteria need to build up to sufficient numbers to start working. The build up time can be reduced by adding a bacterial filter start,. These contain all the nitrifing bacteria in a solution that suspends them in an inactive mode. As so as they are added to water the bacteria start to function and multiply. At this point all ultraviolet filters should be left off to avoid any sterilising effect they may have.

The pond goes through ‘new pond syndrome’ where the addition of excess fish leads to a wipe out or loss of most of the fish. This is caused by the filter not being able to break down the fish waste as it is immature and the fish die as they are swimming in their own waste.

When starting a new pond it should not be stocked heavily for at least four to six weeks to avoid this effect and fish should be added in small numbers after being quarantined first.

Testing the water in new pond will help you to determine when it is safe to add new fish as the start up of the filter follows a simple path.

As the first fish are added the waste is produced as ammonia . this shows on a test kit and the level rises over time until the bacteria appear in sufficient numbers to convert it to nitrite. The nitrite will start to rise as the ammonia is converted and will continue until the bacteria that convert nitrite to nitrate reach the correct numbers and the level then drops. The nitrate level rises until it is either water changed out or used by plants.

The speed at which the filter starts is effected by the water temperature and the amount of oxygen there is available. The higher the oxygen content the faster the filter will establish its self.

Note: Every time you add fish to the pond the filter has to build up more bacteria to help with the increased load. Often this is called shock loading and many filters, especially small filters that are on the limit of their capacity, fail and a complete break down leads to instantaneous waste build up and fish deaths. So when adding a number of fish to your pond always check the levels for a few days to make sure this does not occur.

Sizing the filter.
The creation of a biological filter is very simple and almost any material can be used as a media from gravel to Bio-Block there is no restriction on size or type. As long as you follow the requirements of the bacteria it will work.

Sizing can be difficult as peoples ideas range from 1/3rd the size of the pond to a tiny 25 litre tank.

A rough guide is to allow 1 litre of filter media for 1 gram of food per day. A fish requires 2% of its body weight per day to live a healthy life with normal growth.

So if your pond is to hold say 10 fish at 60cm in length, a fish this size would weight about 3kg.

So a feed weight of 3000 x 2%= 60gms x 10 =600 gms of food per day so a biological filter holding 600 litres of media will be fine.

It is always best to over size your filter as this formula works well when the temperature is constant ( which it never is ) so allow 10-15% extra media to cover any variations or extra fish that find their way in to your pond !

When building a filter allow some extra space around it for extensions should you need it.

Nitrate filters.

The last process of the aerobic filter is the production of nitrate. Although it is not toxic until levels are very high, in excess of 150 mg/ltr, the lower the levels the better it is for the fish, as in their natural habitat it would be less than 1 mg per ltr.

There are three ways to remove nitrate effectively , with a filter , with plants and the last with exchange resin.

Denitrifing filters.
A simple denitrifing filter is a one that supports bacteria that require oxygen free conditions, anaerobic.
Denitrification requires a source of carbon to work, the normal approach to this is to add either methanol or sugar as the supply, the bacteria then break down the carbon source and nitrate to produce carbon dioxide, nitrogen gas and water. (The chemical formula is not quite complete but good enough to show the results in this case)
The filter tank needs to be set up after the normal biological filter to take advantage of the low oxygen and high nitrate content of the water exiting from here. Ideal conditions for denitrifing bacteria are oxygen levels of 2-3mg/ltr and nitrate of 30mg/ltr or more. If levels fall below this hydrogen sulphide will be produced which not only smells like rotten eggs but is also toxic to the fish.

The water needs to spend 2-4 hours passing through the denitrifing filter for it to work( For example if the filter holds 100ltrs the flow rate should be between 200 to 400 ltrs per hour. The outlet should return the water to the beginning if the bio filter to reduce any nitrite that may be in the return water.

This is a difficult system to set up and has a number of problems that can cause major disasters if they go wrong. It is not for the busy person, as it requires time to be spent checking it each day and back washing it weekly to remove the sludge build up that occurs. But it uses nature to do the work and is in general a very good method of nitrate removal.

The most natural way to remove nitrate from the pond water is to use plants. As plants grow they use nitrate to build the leaves and stems that they use to collect sunlight to use to produce food for growth as they grow they require more nitrogen.

The best way to grow plants for vegetable filter is to grow them in a shallow water coarse that is fed from the biological filter, where nitrate production occurs.

The more the plants are cut and removed the more they grow which means they will remove more nitrate. The plants also pick up other toxic metals and chemicals so are also good for purifying the water as well.

The simpler the filter design the better it works as the maintenance is also simple. The vegetable filter should, be large enough for the flow from the bio filter and long so that the water takes a reasonable time to travel through the filter so that the plants have a chance to pick up the nitrate as it goes past in the water. The filter must be free flowing as you don't want it clogging and over flow. The plants will need regular trimming to ensure the maximum growth is achieved. The only down side is the plants do not grow well in the winter months when the weather is cold.

Ion Exchange Resin.
The last method is to use resins that remove nitrate in exchange for another ion usually sodium chloride ( common salt ). The resin is ‘cleaned’ or recharged by washing in a salt solution of 100gms per litre water, each litre of resin needs 5ltires of salt solution to recharge it.

This is the easiest method for removal if the space for vegetable filter is not available , they are compact and very good. The levels can be reduced to less than 25mg/ltr which is often lower than the tap water, used to top the pond up.

It is difficult to say the amount of resin required for each pond but a starting point is 1 litre of resin for each 5000 litres of pond volume, you can always increase the amount of resin if need be, or if it is to much there will be less cleaning.

Ultraviolet systems.

This is probably the least understood and the most poorly sold pond product on the market. It is sold to cure every problem from blanket weed to parasite infestations. When in fact the standard pond unit only cures one pond condition, green water.The idea is to pass the green water through a bath of UV light which then effectively stops the algae's ability to reproduce. The water then clears and all is well, as long as the bulb lasts, then the pond goes green again if the pond plants have not grown enough to compete with the algae.
PIC 10
All UV systems work by circulating pond water around the UV bulb, whether it be the older double ended bulbs or newer single ended type, which is encased within a quartz sleeve which protects the bulb from contact with the water. The outer case directs the water along the out side of the sleeve , ideally in a spiral pattern this allows for the maximum contact time with the UV light, and no water can escape the light therefore giving a better kill rate and higher efficiency. (Although there is only one manufacturer producing such a unit with the spiral flow built in).
UV light is absorbed very quickly and there is a surprising amount of factors which effect the UV’s efficiency.
  1. The speed at which the water flows through the unit, to fast and the contact time will be to short, and to slow and the kill rate will be higher but the algae will grow faster than it can be killed.
  2. Suspended particles in the water, the more debris the water is carrying the more light will be absorbed and the less the work the UVC will do.
  3. Dirt on the quartz sleeve. If the sleeve is dirty the light can not get out to work.
  4. Chemicals in the water. Any dyes that are used as treatments will effect the lights ability to travel through the water.
  5. Poorly designed UV units , This is the biggest cause of UVC not working. There are a number of designs which are very inefficient and should be avoided. Any unit that suspends the bulb above the water is asking for trouble, water can splash on hot the bulb and electric. Units that pump the water through a quartz sleeve are very poor as the amount of UV light that gets from the bulb to the water is so small ( about 10% or less). A properly designed sleeved UV bulb will put about 99% of its output into the water, therefore giving the most efficient and safest use of UV output.
There are two types of Ultraviolet systems that are available, - the standard pond Ultraviolet Clarifier (UVC)PIC 15 and the Ultraviolet Steriliser (UVS)PIC20.

The design of the UVC is very similar but has a number of factors that separate it from the UV sterilisers. A large design difference between them is the gap between the quartz and the outer casing. The UVC is only designed to kill algae so the gap is large, up to 4cm, and allows a high through put and low resistance to small pumps.

The out put near the casing is very low as the water absorbs the UV light, this means the casing material can be thinner than on a UVS.

The gap on a UVS can be as small as 0.5cm, in most cases it is about 1-1.5cm this means the UV level is very much higher and at this dose even bacteria, viruses and parasites can be killed, this dose also takes its toll on the casing as the UV levels are very high therefore UVS are normally made from industrial plastic materials or stainless steel. The flow rate has to drop to very low volumes, as the contact time required to kill bacteria etc is far longer than to kill algae, and this means to service a pond many more UVS would be needed against a UVC just to control algae. This explains the higher cost of sterilisers but they do a totally different job to a Clarifier.

UVS are best put after filters in the return ( if possible) as they work better if the water is free from floating particles, where as UVCs will work on either the dirty or clean side of the filter as the UV dose is less important.

One of the most important factors effecting the UV units are the bulbs they have a relatively short life between 8000 to 9000 hours continuous use.

It is often the aquatic retailers that tell pond keepers that the more UVCs on a pond the better, this is untrue. Once the water is clear it is pointless to have more and more UVCs as they are unable to kill bacteria and parasites as the UV dose is too low and the contact time to short.

There are a few myths about UV systems in general;

1) ‘They sterilise the pond and lower the fish’s immunity to disease’
This is not true as it would be impossible to create a sterile environment in the open area of a garden, and UVC’s do not sterilise at all . UVS only keep water borne diseases under control, not any thing on the fish themselves.

2) ‘UVCs control blanket weed’
This is unlikely as the blanket weed does not pass through the UV chamber.

3) ‘UV’s effect the water chemistry and this can kill the fish’
No tests have been done that prove this and I have never seen any thing to even suggest this could happen.( One of the main reasons UV units are used to sterilise drinking water is that they do not effect the water chemistry).

4) ‘If the bulb is glowing it is still working’
This is also untrue, the reason the manufactures of the bulbs give you a life for optimum use is because they know it lasts this long ! and as the UV light is invisible the fact that it glows and you can see it is not the point.

There is no doubt that Ultraviolet filters play an important part in filtering the pond but, if the biological filters are the correct size and the pond is not over stocked there is no reason that the UV cannot be used for the start of the season and then turned off as the filters start to work.


There is always differences of opinion when it comes to filtration and there will always be the pond which survives with nothing and is ‘perfect’ unfortunately these are few and far between. There is nothing worst than a green pond and with modern pumps and filters there is no excuse for it. If selecting a ready made unit always read the instructions as they will always say the filter will treat a huge pond but if the factors they mention are taken in to account the filters capacity diminishes very quickly and a 10000 litre filter soon only filters a 2500 litre pond and once you have used it taking it back will be difficult.

You can not over filter a pond as it this means is that the filter will take longer between cleaning as it will clog slower if it has a larger surface area. The filter will not be effected by a sudden increases in fish population as the excess filter media will just kick in with out a struggle. This excess filter capacity is a good back up and if the budget will stretch to it is a worth while investment.